Some of the wiring harness may be exposed to sharp metal edges so it pays to protect it.This is especially true in the side box which contains a lot of the relays and fuses.

In several places I found that short lengths of rubber or vinyl tubing could be slit from end to end and slipped over the wires to protect them. (See photo below)

Also make sure the wires that are running back to the tail light assembly are snugly hooked into the tabs that keep them off of the rear wheel.

If you use the search feature you should be able to find other posts that will tell you how to get your headlight switch to work (DOE mandated that it should be always on), the best spark plug to replace the crummy Bosch that comes with the bike and dozens of other improvements we commonly make.